GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Thermithiobacillus tepidarius DSM 3134

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028988594.1 G579_RS0100325 long-chain fatty acid--CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_000423825.1:WP_028988594.1
          Length = 584

 Score =  183 bits (465), Expect = 1e-50
 Identities = 151/486 (31%), Positives = 217/486 (44%), Gaps = 87/486 (17%)

Query: 61  QLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEV 120
           ++ +E  R A  LL +G+ PGDRV I + N+ EW ++  A   VG V V I P Y   E 
Sbjct: 43  EMASEVRRWARGLLALGVRPGDRVAIMAGNSPEWAMLDFAVLSVGAVTVPIYPTYGLTET 102

Query: 121 EYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEA 180
            + L   G  L++   R +    L  LR+ AP       G L   +L       ++ D A
Sbjct: 103 LFVLEDSGASLMLVDGRMQ----LEALRDTAP-------GCLPEGRL-------YVRDPA 144

Query: 181 GQGADEPGLLRFTELIARGNAADPRLAQVA-AGLQATDPINIQFTSGTTGFPKGATLTHR 239
              A   GL  +  L   G   +P L     A +   D   + +TSGT+G+PKG  L+H 
Sbjct: 145 D--AQRAGLPSWEALKDLGERINPELVDARLAAVGREDLATLVYTSGTSGWPKGVMLSHG 202

Query: 240 NILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVL 299
           NIL N       + L P+DR+   +PL H F    G+   +  G  + Y      P T++
Sbjct: 203 NILANIEGFLRVVPLLPSDRVLSFLPLSHVFERGTGHFGAYLAGLEVAYAER---PDTII 259

Query: 300 QTVQDERCTGLHGVPTMF----------IAELDHP------------------------- 324
           + +   R T L  VP +F          +A    P                         
Sbjct: 260 RDLTRARPTILISVPRLFQVLYARLLRDVAGKKGPLGFVLRRGLGLDIGGLVTGQGKGAS 319

Query: 325 RFAEFNL----------STLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           R+   +L            LR  +  G+P P E+ +  +E + L  I   YGMTE SPV 
Sbjct: 320 RWLALHLLRLALHRRLGGRLRFFVSGGAPLPVEIGRFFLE-LGL-PIVEGYGMTEASPVI 377

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
              S + P   R  TVG V P+LE++            G+ GE   +G SVM GYW +E 
Sbjct: 378 ---SANPPGKVRPGTVGPVLPNLELRF-----------GEDGEILVRGPSVMRGYWKNEP 423

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIR-GGENIYPREIEEFLYRHPQVQ 493
            TREA+  GGW+HTGD+  +D  GY+ I  R K++++  GGEN+ P++IE  L  HP + 
Sbjct: 424 ATREAL-AGGWLHTGDVGRLDEAGYLVITDRKKELIVNSGGENVAPQKIEMRLATHPLIN 482

Query: 494 DVQVVG 499
              V G
Sbjct: 483 QAVVFG 488


Lambda     K      H
   0.320    0.136    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 778
Number of extensions: 46
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 584
Length adjustment: 36
Effective length of query: 542
Effective length of database: 548
Effective search space:   297016
Effective search space used:   297016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory